Simple Sequence Repeats Linked with Slow Darkening Trait in Pinto Bean Discovered by Single Nucleotide Polymorphism Assay and Whole Genome Sequencing

Seed coat darkening in pinto bean (Phaseolus vulgaris L.) primarily occurs during prolonged storage and can result in significant loss in value based on it being a consumer perceived product flaw. Several slow darkening (SD) pintos, conditioned by the presence of the recessive sd gene, exist but are poorly adapted. Breeding for improved SD pintos is complicated by the recessive inheritance and expression of the trait in maternal tissue. We sought to develop capacity for marker-assisted selection (MAS) for the SD trait. Three F-2 populations (159 individuals) derived from crosses between SD parents, representing two different sources (1533-15 and SDIP-1) for the trait, and commercial regular darkening (RD) pintos were used to screen for single nucleotide polymorphisms (SNPs) linked with the sd locus. Separate DNA pools from SD and from RD F-2 individuals genotyped for the sd locus were used to detect putative sd-linked SNPs using the bulked-segregant analysis strategy. Two of 1536 SNPs differentiated between the SD and RD DNA bulks for all three populations. The whole genome sequence scaffold possessing the two SNPs was canvassed for simple sequence repeats (SSRs). Three of 12 SSRs from the SNP region distinguished between the SD and RD lines. The three SSRs, Pvsd-1157, Pvsd-1158, and Pvsd-0028, were observed to be tightly linked with the sd locus at 0.9, 0.4, and 3.1 cM, respectively, across the F-2 populations. The SSRs assayed across a recombinant inbred line mapping population (CDC Pintium x 1533-15) placed the sd gene on bean linkage group 7 between framework SSR markers BM210 and PvBR35. A survey of SD and RD advanced lines and cultivars revealed the SSRs will have utility for MAS of the SD trait in pinto bean and perhaps in other dry bean market classes as well.